Here is a solution using latticeExtra(to get ggplot2as a theme), but good luck discerning 90 colors :) (I would try some rcharts-intercat graphs)

library(directlabels)
set.seed(1)
n = 1000
N = 90
dat = data.frame(x=runif(n,1,10),
y=runif(n,1,10),
col=paste0('pop',gl(N,n/N)))
library(latticeExtra)
xyplot(y~x,data=dat,groups=col,
auto.key=list(columns=10),
par.settings = ggplot2like(), axis = axis.grid)
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